It gave extra space in every multiline environment I tried. I'm not really sure what causes it -- I'm looking into it, but it seems the \utilde command really only depends on \fontdimen5. I wonder if that dimension is redefined in a multiline environment....
–
TristanJul 6 '12 at 3:32

I should also add that I'm using the mathptmx package
–
TristanJul 6 '12 at 3:42

Looks like in a normal equation environment, the original \baselineskip is 12pt, while in an aligned environment, the original \baselineskip is 15pt. The \utilde command uses a \baselineskip=1pt command to stack the symbols.
–
TristanJul 6 '12 at 5:36